Bow and stern thruster systems are typically used on large vessels for docking and maneuvering in harbors at low speed. These large vessels are commercial fishing boats, cruise and ocean-going cargo ships. As these multi-axis thruster systems are applied to smaller vessels, such as bass boats, medium size fishing boats, ski boats and small cruisers, a comprehensive control system is required for onboard control of the thruster system as well as remote control of the thruster system and boat for one-person loading and unloading of these smaller boats on and off of trailers. The present invention is a control system that provides this onboard as well as remote control of the thruster system for this purpose.